scPDB - 4mka entry

Protein Data Bank Entry:

PDB ID : 4mka

Resolution :2.050 Å

Experimental Method : X-ray

Deposition Date : 2013-09-04

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Genome polyprotein
ID:	POLG_HCVBK
AC:	P26663
Organism:	Hepatitis C virus genotype 1b
Reign:	Viruses
TaxID:	11105
EC Number:	2.7.7.48

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	23.699
Number of residues:	46
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.799	1174.500

% Hydrophobic	% Polar
34.20	65.80
According to VolSite

Ligand :

HET Code:	2AY
Formula:	C26H26N2O6S
Molecular weight:	494.559 g/mol
DrugBank ID:	-
Buried Surface Area:	63.22 %
Polar Surface area:	119.18 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	2
Rings:	4
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
-9.22637	8.79846	9.113

Binding mode :

What is Poseview ?

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Image generated by PoseView

Protein

Binding Site

Ligand

Interaction pattern

hydrophobic (CA)

aromatic (CZ)

hydrogen bond acceptor (O)

hydrogen bond acceptor/donor (OG)

hydrogen bond donor (N)

positively ionized (NZ)

negatively ionized (OD1)

metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT

Ligand	Protein		Interaction
Atom	Atom	Residue	Distance (Å)	Angle (°)	Type
C32	CB	PRO- 197	4.28	0	Hydrophobic	false
C33	CG	PRO- 197	4.24	0	Hydrophobic	false
C33	CD	ARG- 200	3.85	0	Hydrophobic	false
C34	CD	ARG- 200	3.95	0	Hydrophobic	false
C36	CD	ARG- 200	4.49	0	Hydrophobic	false
O3	ND2	ASN- 291	2.82	170.85	H-Bond (Protein Donor)	false
C8	CB	ASN- 316	4.06	0	Hydrophobic	false
N1	OD1	ASP- 318	2.91	170.5	H-Bond (Ligand Donor)	false
O3	N	ASP- 318	3.44	137.41	H-Bond (Protein Donor)	false
C8	CB	ASP- 319	3.59	0	Hydrophobic	false
C18	CB	CYS- 366	3.97	0	Hydrophobic	false
C34	CB	CYS- 366	3.98	0	Hydrophobic	false
C36	SG	CYS- 366	3.6	0	Hydrophobic	false
C8	SG	CYS- 366	3.74	0	Hydrophobic	false
C34	CB	SER- 368	3.67	0	Hydrophobic	false
C34	CD1	LEU- 384	3.73	0	Hydrophobic	false
C33	CE	MET- 414	4.24	0	Hydrophobic	false
C20	CE	MET- 414	3.7	0	Hydrophobic	false
C32	CZ	TYR- 415	3.61	0	Hydrophobic	false
N26	O	GLN- 446	2.78	163.73	H-Bond (Ligand Donor)	false
O25	N	TYR- 448	2.82	164.25	H-Bond (Protein Donor)	false
C33	CE1	TYR- 448	4	0	Hydrophobic	false
C36	CE1	TYR- 448	3.42	0	Hydrophobic	false
C5	CB	SER- 556	3.63	0	Hydrophobic	false